# This directory provides a unified place for building all kinds of
# GROMACS documentation. This includes some "static" content (Doxygen
# code documentation, reference manual, install guide, old online HTML
-# pages), and content generated from the gmx program for the various
+# images), and content generated from the gmx program for the various
# tools (man and HTML pages). It also provides the "webpage" target,
# that combines all of the above (except man pages in man format) into
# a form suitable for automated deployment to the GROMACS website. It
find_package(PythonInterp)
find_package(Sphinx 1.2.3 COMPONENTS pygments)
-add_subdirectory(old-html)
add_subdirectory(doxygen)
option(GMX_BUILD_WEBPAGE "Whether to try to configure to build the GROMACS static webpages" OFF)
set(SPHINX_SOURCE_FILES
index.rst
download.rst
- online.rst
install-guide/index.rst
man/gromacs.7.rst
user-guide/index.rst
user-guide/getting-started.rst
+ user-guide/flow.rst
user-guide/cutoff-schemes.rst
user-guide/file-formats.rst
user-guide/tools.rst
set(HTML_BUILD_IS_POSSIBLE ON)
# Next, turn it off in any of the preconditions are unsatisified
- if(NOT GMX_BUILD_HELP)
- set(HTML_BUILD_IS_POSSIBLE OFF)
- message(STATUS "Cannot build webpage without GMX_BUILD_HELP=on")
- endif()
-
if(NOT MANUAL_BUILD_IS_POSSIBLE)
set(HTML_BUILD_IS_POSSIBLE OFF)
message(STATUS "Cannot build webpage without being able to build the reference PDF manual")
endif()
endif()
+# TODO Get rid of the remaining content in old-html
+add_custom_target(webpage-old-images
+ ${CMAKE_COMMAND} -E copy_directory ${CMAKE_CURRENT_SOURCE_DIR}/old-html ${HTML_OUTPUT_DIR}
+ COMMENT "Copying flowchart images"
+ VERBATIM
+ )
+
if(HTML_BUILD_IS_POSSIBLE)
# If building the webpage from the repo, then tarballs may not
# exist, and if so, it would not make sense to build that part of
VERBATIM
)
- # TODO Move content from the "old" html output into the new user
- # guide, or delete, as appropriate.
- if(NOT SOURCE_IS_SOURCE_DISTRIBUTION)
- # TODO If content remains here once the user guide is in
- # decent shape, try to make the generated HTML arrive directly
- # in ${HTML_OUTPUT_DIR}
- add_custom_target(webpage-html
- ${CMAKE_COMMAND} -E copy_directory old-html/final ${HTML_OUTPUT_DIR}
- )
- add_dependencies(webpage-html html)
- else()
- # In the source distribution, the html pages are already
- # built, so we can avoid making gmx via the html target
- add_custom_target(webpage-html
- ${CMAKE_COMMAND} -E copy_directory ${CMAKE_CURRENT_SOURCE_DIR}/old-html/final ${HTML_OUTPUT_DIR}
- )
- endif()
-
# The Doxygen configuration in doxygen/Doxyfile-common.cmakein
# makes all the Doxygen output directly in
# ${HTML_OUTPUT_DIR}/doxygen (and makes the directory if it needs
${extra_webpage_dependencies}
VERBATIM
)
- add_dependencies(webpage webpage-sphinx webpage-html doxygen-all)
+ add_dependencies(webpage webpage-sphinx webpage-old-images doxygen-all)
else()
add_custom_target(webpage
COMMAND ${CMAKE_COMMAND} -E echo "Cannot build webpage because of missing requirements. Check cmake status output for reasons"
user-guide/index
- online
-
* `Reference Manual`_ (PDF format)
* Answers to `Frequently Asked Questions <http://www.gromacs.org/Documentation/FAQs>`_
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS is free software; you can redistribute it and/or
-# modify it under the terms of the GNU Lesser General Public License
-# as published by the Free Software Foundation; either version 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-# Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-if (NOT DEFINED GMX_EXECUTABLE OR NOT DEFINED OUTPUT_DIR OR NOT DEFINED SOURCE_HTML_DIR)
- message(FATAL_ERROR "Required input parameter not set")
-endif()
-
-file(MAKE_DIRECTORY ${OUTPUT_DIR})
-file(MAKE_DIRECTORY ${OUTPUT_DIR}/programs)
-file(COPY ${SOURCE_HTML_DIR}/header.html.in DESTINATION .)
-file(COPY ${SOURCE_HTML_DIR}/footer.html DESTINATION .)
-
-# This is generated by gmx help -export html
-set(HEADER_FILE header.html)
-
-execute_process(
- COMMAND ${GMX_EXECUTABLE} -quiet help -export html
- RESULT_VARIABLE exitcode)
-if (exitcode)
- # Ensure that no partial output is left behind.
- file(REMOVE_RECURSE ${OUTPUT_DIR})
- file(REMOVE ${HEADER_FILE})
- message(FATAL_ERROR
- "Failed to generate HTML help. "
- "Set GMX_BUILD_HELP=OFF or GMX_BUILD_HELP=AUTO if you want to skip them.\n"
- "Error/exit code: ${exitcode}")
-endif()
-
-set(FOOTER_FILE ${SOURCE_HTML_DIR}/footer.html)
-file(READ ${HEADER_FILE} HEADER_TEXT)
-file(READ ${FOOTER_FILE} FOOTER_TEXT)
-set(_title_re "[Tt][Ii][Tt][Ll][Ee]")
-
-function(CREATE_HTML_FILE SOURCE_FILE ROOTPATH)
- file(RELATIVE_PATH _rel_path ${SOURCE_HTML_DIR} ${SOURCE_FILE})
- file(READ ${SOURCE_FILE} _content)
- string(REGEX REPLACE "^ *<${_title_re}>(.*)</${_title_re}>\n" "" _content "${_content}")
- set(TITLE "${CMAKE_MATCH_1}")
- string(CONFIGURE "${HEADER_TEXT}" _header @ONLY)
- set(_content "${_header}${_content}${FOOTER_TEXT}")
- file(WRITE ${OUTPUT_DIR}/${_rel_path} "${_content}")
-endfunction()
-
-file(COPY ${SOURCE_HTML_DIR}/images DESTINATION ${OUTPUT_DIR})
-file(MAKE_DIRECTORY ${OUTPUT_DIR}/online)
-file(COPY ${SOURCE_HTML_DIR}/online/style.css DESTINATION ${OUTPUT_DIR}/online)
-file(GLOB _source_files ${SOURCE_HTML_DIR}/online/*.html)
-foreach(_file ${_source_files})
- create_html_file(${_file} "../")
-endforeach()
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS is free software; you can redistribute it and/or
-# modify it under the terms of the GNU Lesser General Public License
-# as published by the Free Software Foundation; either version 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-# Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-include(gmxCustomCommandUtilities)
-
-set(OUTPUT_DIR final)
-
-if (GMX_BUILD_HELP)
- # Unlike the man and completion targets, this target is not built
- # automatically with GMX_BUILD_HELP=AUTO, since most people will not
- # notice it missing.
- file(GLOB_RECURSE deps
- ${CMAKE_CURRENT_SOURCE_DIR}/images/*
- ${CMAKE_CURRENT_SOURCE_DIR}/*.html
- ${CMAKE_CURRENT_SOURCE_DIR}/*.css
- )
- list(APPEND deps
- ${CMAKE_CURRENT_SOURCE_DIR}/BuildHtmlHelp.cmake
- ${CMAKE_CURRENT_SOURCE_DIR}/header.html.in
- )
-
- gmx_add_custom_output_target(html OUTPUT STAMP
- COMMAND ${CMAKE_COMMAND}
- -D GMX_EXECUTABLE=$<TARGET_FILE:gmx>
- -D SOURCE_HTML_DIR=${CMAKE_CURRENT_SOURCE_DIR}
- -D OUTPUT_DIR=${OUTPUT_DIR}
- -P ${CMAKE_CURRENT_SOURCE_DIR}/BuildHtmlHelp.cmake
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- DEPENDS gmx ${deps}
- COMMENT "Generating HTML help")
-
- if (GMX_BUILD_HELP_FORCE)
- set_target_properties(html PROPERTIES EXCLUDE_FROM_ALL OFF)
- endif()
- set_directory_properties(PROPERTIES
- ADDITIONAL_MAKE_CLEAN_FILES "${OUTPUT_DIR};header.html")
-endif()
+++ /dev/null
-
-<P>
-<HR>
-<DIV ALIGN=RIGHT><FONT SIZE="-1">
-<A HREF="http://www.gromacs.org">http://www.gromacs.org</A><BR>
-</FONT></DIV>
-</BODY>
-</HTML>
+++ /dev/null
-<HTML>
-<HEAD>
- <TITLE>@TITLE@</TITLE>
- <LINK rel=stylesheet href="@ROOTPATH@online/style.css" type="text/css">
-</HEAD>
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
- <TABLE WIDTH="98%%">
- <TR>
- <TD WIDTH="116" ROWSPAN="2">
- <A HREF="http://www.gromacs.org/"><IMG SRC="@ROOTPATH@images/gmxlogo_small.jpg" BORDER=0></A>
- </TD>
- <TD ALIGN="LEFT" VALIGN="CENTER" COLSPAN="2">
- <H2>@TITLE@</H2>
- </TD>
- </TR>
- <TR>
- <TD>
- <FONT SIZE="-1"><A HREF="@ROOTPATH@online.html">Main Table of Contents</A></FONT>
- </TD>
- <TD ALIGN="RIGHT" VALIGN="BOTTOM">
- <B>@VERSION@</B>
- </TD>
- </TR>
-</TABLE>
- <HR>
-
+++ /dev/null
-<TITLE>Flow Chart</TITLE>
-<p>This is a flow chart of a typical GROMACS MD run of a protein
-in a box of water.
-A more detailed example is available in the
-<A HREF="../user-guide/index.html#getting-started-with-gromacs">Getting Started</A>
-section. Several steps of energy minimization may be necessary,
-these consist of cycles: grompp -> mdrun.
-<p>
-
-<CENTER>
-<TABLE BORDER=0 CELLMARGIN=0 CELLPADDING=0 CELLSPACING=0>
-
-<TR>
-<TD COLSPAN=2 ALIGN=RIGHT> <A HREF=pdb.html onMouseOver="window.status='Protein Databank file'; return true">eiwit.pdb</A></TD>
-<TD ALIGN=RIGHT> <IMG SRC=../images/flow_leftrightdown.gif></TD>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-</TR>
-
-<TR>
-<TD COLSPAN=2 ALIGN=LEFT>Generate a GROMACS topology </TD>
-<TD></TD>
-<TD BGCOLOR=#777777 COLSPAN=3 ALIGN=CENTER> <A HREF=../programs/gmx-pdb2gmx.html onMouseOver="window.status='Convert PDB file to GROMAX coordinate file and topology'; return true"><B>gmx pdb2gmx</B></A> </TD>
-<TD><IMG SRC=../images/flow_vrule.gif></TD>
-</TR>
-
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif BORDER=0></TD>
-<TD WIDTH=20></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><A HREF=gro.html onMouseOver="window.status='GROMACS coordinate file containing molecules from PDB file'; return true">conf.gro</A></TD>
-<TD></TD>
-<TD ALIGN=CENTER> <A HREF=top.html onMouseOver="window.status='GROMACS ascii topology file'; return true">topol.top</A> </TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif BORDER=0></TD>
-<TD></TD>
-<TD ROWSPAN=5 COLSPAN=1 ALIGN=CENTER><IMG SRC=../images/flow_vline.gif><BR><IMG SRC=../images/flow_vline.gif><BR><IMG SRC=../images/flow_vline.gif><BR><IMG SRC=../images/flow_vline.gif><BR><IMG SRC=../images/flow_down.gif></TD>
-</TR>
-
-<TR>
-<TD COLSPAN=2 ALIGN=left>Enlarge the box</TD>
-<TD></TD>
-<TD ALIGN=CENTER BGCOLOR=#777777> <A HREF=../programs/gmx-editconf.html onMouseOver="window.status='Adjust boxsize and placement of molecule'; return true"><B>gmx editconf</B></A> </TD>
-<TD></TD>
-<TD><IMG SRC=../images/flow_vrule.gif></TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
-<TD></TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER> <A HREF=gro.html onMouseOver="window.status='GROMACS coordinate file with adjusted box etc.'; return true">conf.gro</A> </TD>
-<TD></TD>
-</TR>
-
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
-<TD></TD>
-</TR>
-
-<TR>
-<TD COLSPAN=2 ALIGN=LEFT>Solvate protein</TD>
-<TD></TD>
-<TD COLSPAN=3 ALIGN=CENTER BGCOLOR=#777777> <A HREF=../programs/gmx-solvate.html onMouseOver="window.status='Fill box with water (solvate molecule)'; return true"><B>gmx solvate</B></A> </TD>
-<TD><IMG SRC=../images/flow_vrule.gif></TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><A HREF=gro.html onMouseOver="window.status='GROMACS coordinate file with water molecules added'; return true">conf.gro</A></TD>
-<TD></TD>
-<TD ALIGN=CENTER> <A HREF=top.html onMouseOver="window.status='GROMACS ascii topology file with water molecules added'; return true">topol.top</A> </TD>
-</TR>
-
-<TR>
-<TD COLSPAN=2 ALIGN=RIGHT><A HREF=mdp.html onMouseOver="window.status='Parameter file for grompp (controls all MD parameters)'; return true">grompp.mdp</A></TD>
-<TD ALIGN=RIGHT> <IMG SRC=../images/flow_leftrightdown.gif></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
-<TD></TD>
-</TR>
-
-
-<TR>
-<TD COLSPAN=2 ALIGN=LEFT>Generate mdrun input file</TD>
-<TD></TD>
-<TD COLSPAN=3 ALIGN=CENTER BGCOLOR=#777777> <A HREF=../programs/gmx-grompp.html onMouseOver="window.status='Process parameters, coordinates and topology and write binary topology'; return true"><B>gmx grompp</B></A> </TD>
-<TD><IMG SRC=../images/flow_vrule.gif></TD>
-<TD></TD>
-<TD></TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
-<TD ROWSPAN=3 ALIGN=RIGHT>
-<IMG SRC=../images/flow_rightleftdown.gif></TD>
-<TD ALIGN=CENTER VALIGN=BOTTOM>Continuation</TD>
-</TR>
-
-<TR>
-<TD COLSPAN=2 ALIGN=LEFT></TD>
-<TD></TD>
-<TD COLSPAN=3 ALIGN=CENTER> <A HREF=tpr.html onMouseOver="window.status='Portable GROMACS binary run input file (contains all information to start MD run)'; return true">topol.tpr</A></TD>
-<TD ALIGN=CENTER > <A HREF=cpt.html onMouseOver="window.status='Checkpoint file'; return true">state.cpt</A> </TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
-<TD ROWSPAN=2 ALIGN=CENTER>
-<IMG SRC=../images/flow_vline.gif><BR>
-<IMG SRC=../images/flow_leftup.gif></TD>
-</TR>
-
-<TR>
-<TD COLSPAN=2>Run the simulation (EM or MD)</TD>
-<TD></TD>
-<TD COLSPAN=3 ALIGN=CENTER BGCOLOR=#777777> <A HREF=../programs/gmx-mdrun.html onMouseOver="window.status='The moment you have all been waiting for! START YOUR MD RUN'; return true"><B>gmx mdrun</B></A> </TD>
-<TD></TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER> <A HREF=xtc.html onMouseOver="window.status='Portable compressed trajectory'; return true">traj.xtc</A> /
-<A HREF=trr.html onMouseOver="window.status='Full precision portable trajectory'; return true">traj.trr</A> </TD>
-<TD></TD>
-<TD ALIGN=CENTER> <A HREF=edr.html onMouseOver="window.status='Portable energy file'; return true">ener.edr</A> </TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
-</TR>
-
-<TR>
-<TD COLSPAN=2 ALIGN=LEFT>Analysis</TD>
-<TD></TD>
-<TD ALIGN=CENTER BGCOLOR=#777777> <A HREF=../online.html onMouseOver="window.status='Your favourite GROMACS analysis tool'; return true"><B>g_...</B></A> <BR> <A HREF=../programs/gmx-view.html onMouseOver="window.status='gmx view, the GROMACS trajectory viewer'; return true"><B>gmx view</B></A> </TD>
-<TD></TD>
-<TD ALIGN=CENTER BGCOLOR=#777777> <A HREF=../programs/gmx-energy.html onMouseOver="window.status='Energy plots, averages and fluctuations'; return true"><B>gmx energy</B></A> </TD>
-<TD><IMG SRC=../images/flow_vrule.gif></TD>
-</TR>
-
-
-</TABLE>
-</CENTER>
+++ /dev/null
-H1 { text-indent: 0em; font-size: 24pt; font-family: serif }
-H2 { text-indent: 0em; font-size: 24pt; font-weight: bold; font-family: arial,helvetica,verdana,sans-serif }
-H3 { text-indent: 0em; font-size: 18pt; font-weight: bold; font-family: arial,helvetica,verdana,sans-serif }
-H4 { font-family: arial,helvetica,verdana,sans-serif }
-A:link { text-decoration: none }
-A:active { text-decoration: none }
-A:visited { text-decoration: none }
-tt { font-family: courier,"lucida console",serif }
-
-
-
-
-
-
-
+++ /dev/null
-Online reference
-================
-
-* `Flow Chart <online/flow.html>`_
--- /dev/null
+Flow Chart
+==========
+
+This is a flow chart of a typical GROMACS MD run of a protein
+in a box of water.
+A more detailed example is available in :doc:`getting-started`.
+Several steps of energy minimization may be necessary,
+these consist of cycles: :ref:`gmx grompp` -> :ref:`gmx mdrun`.
+
+.. raw:: html
+
+ <CENTER>
+ <TABLE BORDER=0 CELLMARGIN=0 CELLPADDING=0 CELLSPACING=0>
+
+ <TR>
+ <TD COLSPAN="2" STYLE="text-align:right"> <A HREF="file-formats.html#pdb" onMouseOver="window.status='Protein Databank file'; return true">eiwit.pdb</A></TD>
+ <TD STYLE="text-align:right"><IMG SRC=../images/flow_leftrightdown.gif></TD>
+ <TD></TD>
+ <TD></TD>
+ <TD></TD>
+ </TR>
+
+ <TR>
+ <TD COLSPAN=2>Generate a GROMACS topology </TD>
+ <TD></TD>
+ <TD BGCOLOR=#777777 COLSPAN=3 STYLE="text-align:center"><A HREF=../programs/gmx-pdb2gmx.html onMouseOver="window.status='Convert PDB file to GROMAX coordinate file and topology'; return true"><B>gmx pdb2gmx</B></A></TD>
+ <TD><IMG SRC=../images/flow_vrule.gif></TD>
+ </TR>
+
+
+ <TR>
+ <TD></TD>
+ <TD></TD>
+ <TD></TD>
+ <TD STYLE="text-align:center"><IMG SRC=../images/flow_vline.gif BORDER=0></TD>
+ <TD WIDTH=20></TD>
+ <TD STYLE="text-align:center"><IMG SRC=../images/flow_vline.gif></TD>
+ </TR>
+
+ <TR>
+ <TD></TD>
+ <TD></TD>
+ <TD></TD>
+ <TD STYLE="text-align:center"><A HREF="file-formats.html#gro" onMouseOver="window.status='GROMACS coordinate file containing molecules from PDB file'; return true">conf.gro</A></TD>
+ <TD></TD>
+ <TD STYLE="text-align:center"> <A HREF="file-formats.html#top" onMouseOver="window.status='GROMACS ascii topology file'; return true">topol.top</A> </TD>
+ </TR>
+
+ <TR>
+ <TD></TD>
+ <TD></TD>
+ <TD></TD>
+ <TD STYLE="text-align:center"><IMG SRC=../images/flow_down.gif BORDER=0></TD>
+ <TD></TD>
+ <TD ROWSPAN=5 COLSPAN=1 STYLE="text-align:center"><IMG SRC=../images/flow_vline.gif><BR><IMG SRC=../images/flow_vline.gif><BR><IMG SRC=../images/flow_vline.gif><BR><IMG SRC=../images/flow_vline.gif><BR><IMG SRC=../images/flow_down.gif></TD>
+ </TR>
+
+ <TR>
+ <TD COLSPAN=2>Enlarge the box</TD>
+ <TD></TD>
+ <TD STYLE="text-align:center" BGCOLOR=#777777><A HREF=../programs/gmx-editconf.html onMouseOver="window.status='Adjust boxsize and placement of molecule'; return true"><B>gmx editconf</B></A></TD>
+ <TD></TD>
+ <TD><IMG SRC=../images/flow_vrule.gif></TD>
+ </TR>
+
+ <TR>
+ <TD></TD>
+ <TD></TD>
+ <TD></TD>
+ <TD STYLE="text-align:center"><IMG SRC=../images/flow_vline.gif></TD>
+ <TD></TD>
+ </TR>
+
+ <TR>
+ <TD></TD>
+ <TD></TD>
+ <TD></TD>
+ <TD STYLE="text-align:center"> <A HREF="file-formats.html#gro" onMouseOver="window.status='GROMACS coordinate file with adjusted box etc.'; return true">conf.gro</A> </TD>
+ <TD></TD>
+ </TR>
+
+
+ <TR>
+ <TD></TD>
+ <TD></TD>
+ <TD></TD>
+ <TD STYLE="text-align:center"><IMG SRC=../images/flow_down.gif></TD>
+ <TD></TD>
+ </TR>
+
+ <TR>
+ <TD COLSPAN=2>Solvate protein</TD>
+ <TD></TD>
+ <TD COLSPAN=3 STYLE="text-align:center" BGCOLOR=#777777> <A HREF=../programs/gmx-solvate.html onMouseOver="window.status='Fill box with water (solvate molecule)'; return true"><B>gmx solvate</B></A> </TD>
+ <TD><IMG SRC=../images/flow_vrule.gif></TD>
+ </TR>
+
+ <TR>
+ <TD></TD>
+ <TD></TD>
+ <TD></TD>
+ <TD STYLE="text-align:center"><IMG SRC=../images/flow_vline.gif></TD>
+ <TD></TD>
+ <TD STYLE="text-align:center"><IMG SRC=../images/flow_vline.gif></TD>
+ </TR>
+
+ <TR>
+ <TD></TD>
+ <TD></TD>
+ <TD></TD>
+ <TD STYLE="text-align:center"><A HREF="file-formats.html#gro" onMouseOver="window.status='GROMACS coordinate file with water molecules added'; return true">conf.gro</A></TD>
+ <TD></TD>
+ <TD STYLE="text-align:center"> <A HREF="file-formats.html#top" onMouseOver="window.status='GROMACS ascii topology file with water molecules added'; return true">topol.top</A> </TD>
+ </TR>
+
+ <TR>
+ <TD COLSPAN=2 STYLE="text-align:right"><A HREF="file-formats.html#mdp" onMouseOver="window.status='Parameter file for grompp (controls all MD parameters)'; return true">grompp.mdp</A></TD>
+ <TD STYLE="text-align:right"> <IMG SRC=../images/flow_leftrightdown.gif></TD>
+ <TD STYLE="text-align:center"><IMG SRC=../images/flow_down.gif></TD>
+ <TD></TD>
+ <TD STYLE="text-align:center"><IMG SRC=../images/flow_down.gif></TD>
+ <TD></TD>
+ </TR>
+
+
+ <TR>
+ <TD COLSPAN=2>Generate mdrun input file</TD>
+ <TD></TD>
+ <TD COLSPAN=3 STYLE="text-align:center" BGCOLOR=#777777><A HREF=../programs/gmx-grompp.html onMouseOver="window.status='Process parameters, coordinates and topology and write binary topology'; return true"><B>gmx grompp</B></A></TD>
+ <TD><IMG SRC=../images/flow_vrule.gif></TD>
+ <TD></TD>
+ <TD></TD>
+ </TR>
+
+ <TR>
+ <TD></TD>
+ <TD></TD>
+ <TD></TD>
+ <TD></TD>
+ <TD STYLE="text-align:center"><IMG SRC=../images/flow_vline.gif></TD>
+ <TD ROWSPAN=3 STYLE="text-align:right"><IMG SRC=../images/flow_rightleftdown.gif></TD>
+ <TD STYLE="text-align:center;vertical-align:bottom">Continuation</TD>
+ </TR>
+
+ <TR>
+ <TD COLSPAN=2></TD>
+ <TD></TD>
+ <TD COLSPAN=3 STYLE="text-align:center"> <A HREF="file-formats.html#tpr" onMouseOver="window.status='Portable GROMACS binary run input file (contains all information to start MD run)'; return true">topol.tpr</A></TD>
+ <TD STYLE="text-align:center"><A HREF="file-formats.html#cpt" onMouseOver="window.status='Checkpoint file'; return true">state.cpt</A></TD>
+ </TR>
+
+ <TR>
+ <TD></TD>
+ <TD></TD>
+ <TD></TD>
+ <TD></TD>
+ <TD STYLE="text-align:center"><IMG SRC=../images/flow_down.gif></TD>
+ <TD ROWSPAN=2 STYLE="text-align:center">
+ <IMG SRC=../images/flow_vline.gif><BR>
+ <IMG SRC=../images/flow_leftup.gif></TD>
+ </TR>
+
+ <TR>
+ <TD COLSPAN=2>Run the simulation (EM or MD)</TD>
+ <TD></TD>
+ <TD COLSPAN=3 STYLE="text-align:center" BGCOLOR=#777777> <A HREF=../programs/gmx-mdrun.html onMouseOver="window.status='The moment you have all been waiting for! START YOUR MD RUN'; return true"><B>gmx mdrun</B></A> </TD>
+ <TD></TD>
+ </TR>
+
+ <TR>
+ <TD></TD>
+ <TD></TD>
+ <TD></TD>
+ <TD STYLE="text-align:center"><IMG SRC=../images/flow_vline.gif></TD>
+ <TD></TD>
+ <TD STYLE="text-align:center"><IMG SRC=../images/flow_vline.gif></TD>
+ </TR>
+
+ <TR>
+ <TD></TD>
+ <TD></TD>
+ <TD></TD>
+ <TD STYLE="text-align:center"> <A HREF="file-formats.html#xtc" onMouseOver="window.status='Portable compressed trajectory'; return true">traj.xtc</A> /
+ <A HREF="file-formats.html#trr" onMouseOver="window.status='Full precision portable trajectory'; return true">traj.trr</A> </TD>
+ <TD></TD>
+ <TD STYLE="text-align:center"> <A HREF="file-formats.html#edr" onMouseOver="window.status='Portable energy file'; return true">ener.edr</A> </TD>
+ </TR>
+
+ <TR>
+ <TD></TD>
+ <TD></TD>
+ <TD></TD>
+ <TD STYLE="text-align:center"><IMG SRC=../images/flow_down.gif></TD>
+ <TD></TD>
+ <TD STYLE="text-align:center"><IMG SRC=../images/flow_down.gif></TD>
+ </TR>
+
+ <TR>
+ <TD COLSPAN=2>Analysis</TD>
+ <TD></TD>
+ <TD STYLE="text-align:center" BGCOLOR=#777777><A HREF="../programs/bytopic.html" onMouseOver="window.status='Your favourite GROMACS analysis tool'; return true"><B>g_...</B></A><BR><A HREF=../programs/gmx-view.html onMouseOver="window.status='gmx view, the GROMACS trajectory viewer'; return true"><B>gmx view</B></A></TD>
+ <TD></TD>
+ <TD STYLE="text-align:center" BGCOLOR=#777777><A HREF=../programs/gmx-energy.html onMouseOver="window.status='Energy plots, averages and fluctuations'; return true"><B>gmx energy</B></A></TD>
+ <TD><IMG SRC=../images/flow_vrule.gif></TD>
+ </TR>
+
+
+ </TABLE>
+ </CENTER>
+
Getting started
===============
+.. toctree::
+ :hidden:
+
+ flow
+
In this chapter we assume the reader is familiar with Molecular Dynamics and
familiar with Unix, including the use of a text editor such as ``jot``, ``emacs``
or ``vi``. We furthermore assume the |Gromacs| software is installed properly on
Flowchart of typical simulation
-------------------------------
-A typical simulation workflow with |Gromacs| is `illustrated here <../online/flow.html>`_.
+A typical simulation workflow with |Gromacs| is :doc:`illustrated here <flow>`.
Important files
---------------
}
}
-/********************************************************************
- * HelpExportHtml
- */
-
-/*! \internal
- * \brief
- * Implements export for HTML help.
- *
- * This whole class can go once docs/old-html/ no longer requires header.html
- * that it generates.
- *
- * \ingroup module_commandline
- */
-class HelpExportHtml : public HelpExportInterface
-{
- public:
- //! Initializes HTML exporter.
- HelpExportHtml();
-
- virtual void startModuleExport() {}
- virtual void exportModuleHelp(
- const CommandLineModuleInterface & /*module*/,
- const std::string & /*tag*/,
- const std::string & /*displayName*/) {}
- virtual void finishModuleExport() {}
-
- virtual void startModuleGroupExport() {}
- virtual void exportModuleGroup(const char * /*title*/,
- const ModuleGroupContents & /*modules*/) {}
- virtual void finishModuleGroupExport() {}
-};
-
-HelpExportHtml::HelpExportHtml()
-{
- std::string header = gmx::File::readToString("header.html.in");
- header = replaceAll(header, "@VERSION@", gmx_version());
- gmx::File::writeFileFromString("header.html", header);
-}
-
/********************************************************************
* HelpExportReStructuredText
*/
// Add internal topics lazily here.
addTopic(HelpTopicPointer(new CommandsHelpTopic(*impl_)));
- const char *const exportFormats[] = { "html", "rst", "completion" };
+ const char *const exportFormats[] = { "rst", "completion" };
std::string exportFormat;
Options options(NULL, NULL);
options.addOption(StringOption("export").store(&exportFormat)
if (!exportFormat.empty())
{
boost::scoped_ptr<HelpExportInterface> exporter;
- if (exportFormat == "html")
- {
- exporter.reset(new HelpExportHtml());
- }
- else if (exportFormat == "rst")
+ if (exportFormat == "rst")
{
exporter.reset(new HelpExportReStructuredText(*impl_));
}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff
